BIOE3100 Exam 1

Engineering Analysis of Physiological Processes: Chapters 1-6

Physiology

Study of the normal functioning of a living organism and its component parts

Wolfe’s Law

Form follows function. Function explains the “why” and the process or mechanism describes the “how”.

Homeostasis

Regulation of the body’s internal environment. “Dynamic disequilibrium”

Law of mass balance

Amount remains constant if input is offset by loss.

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Total amount of substance X in body = Intake + Production - Excretion - Metabolism

Mass flow

Mass Flow = Concentration of Z \* Volume flow

Amount Z/min = (Amount Z/vol) \* (vol/min)

Simple control system

Regulated variables are kept within normal range by control mechanisms.

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Two types:

* Local control restricted to a tissue
* Reflex control for long-distance pathway i.e. nervous and/or endocrine systems

Negative feedback

Response counteracts stimulus, stopping loop. Stabilizes variable.

Positive feedback

Response reinforces stimulus, sending variable away from setpoint. Reinforces stimulus.

Feedforward control

Anticipates change.

Acclimatization

Naturally

Acclimation

In a laboratory setting.

Three major cavities

Cranial, thoracic (pleural sac & pericardial sac) separated by the abdominopelvic cavity (abdominal & pelvic cavity)

Fluid-filled compartments

Circulatory system, eyes, cerebrospinal fluid (CSF)

Hollow organs

Organs that have a small or narrow cavity or lumen inside them.

i.e. heart, lungs, blood vessels, intestines

Function of cell membrane

1. Physical isolation
2. Regulation of exchange with the environment
3. Communication between the cell and its environment
4. Structural support

Cell membrane composition

Lipids (phospholipids, sphingolipids, cholesterol), proteins (integral i.e. transmembrane & lipid-anchored, peripheral), and carbohydrates (glycoproteins, glycolipids).

Cholesterol + Phospholipids

Lipid bilayers which function as a selective barrier between cytosol and external environment.

Sphingolipids + Carbohydrates

Glycolipids whose functions include structural stability, cell recognition, and immune system.

Carbohydrates + Proteins

Glycoproteins whose functions include structural stability, cell recognition, and immune system.

Fluid mosaic model

Scientific model that describes a cell membrane.

Cell composition

Nucleus, cell membrane, and cytoplasm.

The cytoplasm is composed of:


1. Cytosol
2. Membranous organelles


1. Mitochondria
2. Endoplasmic reticulum
3. Golgi apparatus
4. Lysosomes
5. Peroxisomes
3. Inclusions (NO Membranes)


1. Liquid droplets
2. Glycogen granules
3. Ribosomes (fixed & free)
4. Protein fibers


1. Cytoskeleton
2. Centrioles
3. Cilia
4. Flagella

Cytoplasmic protein fibers

* Actin (microfilaments)
* Intermediate filaments
* Keratin
* Neurofilaments
* Microtubules
* Centrioles - Direct DNA movement in cell division
* Cilia - Fluid movement across cells
* Flagella - Cell movement through fluid

Motor proteins

Myosins - Muscle contraction

Kinesins & Dyneins - Movement of vesicles along microtubules

Dyneins - Movement of cilia and flagella

Mitochondria

Two membranes create two compartments

* Mitochondrial matrix
* Unique DNA
* Intermembrane space
* Essential role in cellular ATP production

Endoplasmic Reticulum (ER)

Rough ER

* Ribosomes attached
* Protein assembly and modification

Smooth ER

* Synthesis of fatty acid, steroids, lipids
* Modified forms in liver, kidney, muscles

Golgi Apparatus

* Stacked sacs surrounded by vesicles
* Modifies protein made on rough ER
* Packages into vesicles

Cytoplasmic Vesicles

* Secretory vesicles
* Released from cell
* Storage vesicles
* Lysosomes
* Enzymes to degrade bacteria or old organelles
* Acidic interior
* Lysosomal storage diseases

Cytoplasmic Vesicles

* Peroxisomes
* Enzymes to degrade long-chain fatty acids and toxic foreign molecules
* Generate and breakdown hydrogen peroxide

Nucleus

* Nuclear envelope: two membranes
* Nuclear pore complex
* Chromatin: DNA and associated proteins
* Nucleoli
* Control synthesis of ribosomal RNA

Protein synthesis

1. mRNA is transcribed from genes in the DNA
2. mRNA leaves the nucleus and attaches to cytosolic ribosomes, initiating protein synthesis
3. Some proteins are released by free ribosomes into the cytosol or are targeted to specific organelles
4. Ribosomes attached to the rough ER direct proteins destined for packaging into the lumen of the rough ER
5. Proteins are modified as they pass through the lumen of the ER
6. Transport vesicles move the proteins from the ER to the golgi apparatus
7. Golgi cisternae migrate toward the cell membrane
8. Some vesicles bud off the cisternae and move in a retrograde or backward direction
9. Some vesicles bud off to form lysosomes or storage vesicles
10. Other vesicles become secretory vesicles that release their contents outside the cell

Primary tissue types

Epithelial, connective, muscle, neural/nerve

Extracellular matrix

* Synthesized and secreted by cells
* Proteoglycans
* Glycoproteins covalently bound to polysaccharides
* Insoluble protein fibers
* Examples: collagen, fibronectin, laminin
* Strength
* Anchor cells to matrix for communication

Cell Junctions and Cell Adhesion Molecules (CAMs)

* Cell-cell junctions
* Gap junction (communicating junction)
* Tight junction (occluding junction)
* Anchoring junction

Five functional categories of epithelia

Exchange, transporting, ciliated, protective, secretory.

Exchange epithelia

Thin, flat cells of exchange epithelium allow movement through and between the cells.

Transporting epithelia

Selectively move substances between a lumen and the ECF.

Ciliated epithelia

Beating cilia create fluid currents that sweep across the epithelial surface.

Protective epithelia

Have many stacked layers of cells that are constantly being replaced.

Secretory epithelia

Make and release a product.

Exocrine secretions such as the mucus shown here, are secreted outside the body.

The secretions of endocrine cells (hormones) are released into the blood.

Connective tissue cells

Extensive matrix with varied matrix and cartilage has no blood supply.

Mobile cells

* Blood cells (red & white)

Fixed

* Macrophages
* Adipocytes
* Fibroblasts

Connective tissue matrix

Ground substance

* Mineralized (bone)
* Gelatinous/Syrupy
* Loose connective tissue
* Dense connective tissue
* Cartilage
* Adipose tissue
* Watery (blood plasma)


* Protein Fibers
* Fibronectin (connects cells to matrix)
* Fibrillin (forms filaments and sheets)
* Elastin (stretch and recoil)
* Collagen (stiff but flexible)

Loose connective tissues

Elastic tissues under skin.

Ground substance is the ECM.

Tissue that is very flexible with multiple cell types and fibers.

Dense connective tissues

Tendons (connect skeletal muscles to bone)

Ligaments (connect bones to bones)

Collagen fibers of tendon are densely packed into parallel bundles.

Supporting connective tissues

* Cartilage
* Solid & flexible
* Lacks blood supply
* Nose, ears, knee, windpipe/trachea
* Bone
* Calcified
* Strong & rigid

Hard bone forms when osteoblasts deposit calcium phosphate crystals in the matrix. Cartilage has firm but flexible matrix secreted by cells called chondrocytes.

Additional connective tissues

* Adipocytes
* Adipose connective tissue
* White (single liquid droplet)
* Brown (white liquid droplets)
* Blood
* Plasma matrix
* Free blood cells

In white fat, the cell cytoplasm is almost entirely filled with liquid droplets.

Blood consists of liquid matrix plus red and white blood cells and the cell fragments called platelets.

Muscle tissues

Excitable and contractile (force and movement)

Minimal matrix with external lamina that can generate electrical signals, force, and movement.

There are three types:

* Cardiac
* Smooth
* Skeletal

Nervous tissues

Neurons (nerve cells) that send signals & are excitable.

Glial cells (neuroglia) support.

Minimal matrix with external lamina that can generate electrical signals.

Tissue remodeling includes

* Cell death
* Necrosis (death from injury)
* Apoptosis (programmed cell death)
* Stem cells
* Totipotent
* Pluripotent
* Multipotent

Organs

Groups of tissues with related function i.e. skin

Properties of living organisms

1. Have a complex structure whose basic unit of organization is the cell
2. Acquire, transform, store, and use energy
3. Sense and respond to internal and external environments
4. Maintain homeostasis through internal control systems with feedback
5. Store, use, and transmit information
6. Reproduce, develop, grow, and die
7. Have emergent properties that cannot be predicted from the simple sum of the parts
8. Individuals adapt and species evolve

Work

Chemical work - the making and breaking of chemical bonds

Transport work - moving ions, molecules, and larger particles.

* Useful for creating concentration gradients

Mechanical work - moving organelles, changing cell shape, beating flagella and cilia

* Contracting muscles

Energy

Kinetic energy

* Energy of motion
* Work involves movement

Potential energy

* Stored energy
* In concentration gradients and chemical bonds
* Must be converted to kinetic energy to perform work
* Transformation efficiency

1st law of thermo

Total amount of energy in the universe is constant.

2nd law of thermo

Processes move from state of order to randomness or disorder (entropy).

Reactants and products of combination reactions

A+B → C

Reactants and products of decombination reactions

C → A+B

Reactants and products of single displacement reactions

L + MX → LX + M where X represents atoms, ions, or chemical groups.

Reactants and products of double displacement reactions

LX + MY → LY + MX where X and Y represents atoms, ions, or chemical groups.

Activation energy

The “push” needed to start a reaction

Exergonic reaction

Release energy because the products have less energy than the reactants.

Endergonic reaction

Trap some activation energy in the products, which then have more free energy than the reactants.

Enzymes

Speed up the rate of chemical reactions

* Catalysts
* Reactants (substrates)

Can be activated, inactivated, or modulated

Isozymes

Catalyze same reaction, but under different conditions. Diagnostic enzymes

Oxidation-reduction reaction

Add or subtract electrons.

* Transfer electrons from donor to oxygen
* Remove electrons and H+
* Gain electrons

Hydrolysis-dehydration reaction

Add or subtract a water molecule

* Split large molecules by adding water
* Remove water to make one large molecule from several smaller ones

Addition-subtraction-exchange reaction

Exchange groups between molecules

Add or subtract groups

Ligation reaction

Join two substrates using energy from ATP

Metabolism

All chemical reactions that take place in an organism.

Metabolism regulation

1. Controlling enzyme concentrations
2. Producing modulators that change reaction rates


1. Feedback inhibition
3. Using different enzymes to catalyze reversible reactions
4. Compartmentalizing enzymes within organelles
5. Maintaining optimum ratio of ATP to ADP

Reversible reactions

Reversible reactions are chemical reactions that can proceed in both forward and reverse directions. They involve the conversion of reactants into products and the conversion of products back into reactants. The reaction can reach a state of equilibrium where the forward and reverse reactions occur at the same rate. This allows for the possibility of the reaction to be reversed under certain conditions.

Irreversible reactions

Lack the enzyme for reverse direction.

Catabolic pathways that produce ATP

1. Glycolysis
2. Citric acid cycle
3. Electron transport chain

Anaerobic metabolism

0 NADPH and 2 ATP

Aerobic metabolism

6 H2O, 30-32 ATP, and 6 CO2

Codons in genetic code

64

Protein synthesis

Converts genetic code of DNA into a functional protein.


1. Gene activation
2. Transcription
3. mRNA processing
4. Translation
5. Post-translational modification

Transcription

1. RNA polymerase binds to DNA
2. The section of DNA that contains the gene unwinds
3. RNA bases bind to DNA, creating a single strand of mRNA
4. mRNA and the RNA polymerase detach from DNA, and the mRNA goes to the cytosol after processing.

Translation

1. Transcription
2. mRNA processing - processed mRNA leaves nucleus and associates with ribosomes
3. Attachment of ribosomal subunits
4. Translation - Each tRNA molecule attaches at one end to a specific amino acid. Anticodon of tRNA molecule pairs with appropriate codon on the mRNA, allowing amino acids to be linked in the order specified by mRNA code.
5. Termination

Translation components

* mRNA, rRNAs, and tRNAs
* Ribosomes and amino acids

What are the post-translation modifications that proteins may undergo?

1. Protein folding
2. Cross-linkage
3. Cleavage
4. Addition of other molecules or groups
5. Assembly into polymeric proteins

Intracellular fluid

2/3 of the total body water volume

Extracellular fluid

is 1/3 of the total body water volume and consists of the interstitial fluid and blood plasma.

Osmosis

Movement of water across a membrane in response to a solute concentration gradient

Aquaporins

Transport water across cell membranes in response to osmotic gradients.

Osmolarity

Expresses number of particles

Molarity

Expresses concentration

Hypotonic

Higher concentration of non-penetrating molecules than net movement of water into cell

Hypertonic

Lower concentration of non-penetrating molecules than net movement of water into cell

Isotonic

Equal concentration of non-penetrating molecules and net movement of water into cell

Tonicity

Refers to the relative concentration of solutes in two solutions separated by a semipermeable membrane

Rules for osmolarity and tonicity

1. Assume all intracellular solutes are non-penetrating
2. Compare osmolarities before cell is exposed to the solution
3. Tonicity of a solution describes the volume change of a cell at equilibrium
4. Determine tonicity by comparing non-penetrating solute concentrations in the cell and the solution. Net water movement is into the compartment with the higher concentration of non-penetrating solutes.
5. Hyposmotic solutions are always hypotonic

Bulk flow

Fluids are gases and liquids

* pressure gradients

Methods of passive transport

* Simple diffusion (concentration gradient)
* Protein-mediated
* Facilitated diffusion (concentration gradient)
* Ion channel (electrochemical gradient)
* Aquaporin channel (osmosis)

Methods of active transport

* Vesicular transport (ATP)
* Exocytosis
* Endocytosis
* Phagocytosis
* Protein-mediated
* Direct or primary active transport (ATPases)
* Indirect or secondary active transport (concentration gradient created by ATP)

Rules for Diffusion

General Properties of Diffusion


1. Diffusion uses kinetic energy of molecular movement -- does not require external source
2. Molecules diffuse from areas of high concentration to low concentration
3. Diffusion continues until concentrations reach equilibrium
4. Diffusion is faster if:


1. higher concentration gradients
2. over shorter distances
3. at higher temperatures
4. for smaller molecules
5. Can take place in an open system or across a partition that separates to systems

Simple Diffusion across a membrane


6. Rate of diffusion faster if:


1. Membrane’s SA is longer
2. Membrane is thinner
3. Concentration gradient is larger
4. Membrane is more permeable to molecule
7. Membrane permeability to a molecule depends on


1. Molecule’s lipid solubility
2. Molecule’s size
3. Lipid composition of membrane

Functions of membrane proteins

Structural proteins

* Create & maintain cell-junctions
* Maintain cell shape
* Attach cells to ECM

Enzymes

* Catalyze reactions outside of membrane
* Membrane receptor proteins

Transporters

* Channel proteins - water-filled tubes
* Form open & gated channels
* Carrier proteins - bind substrate. NO tubes.
* Change confirmation

What are the types of channels

1. Water channels
2. Ion channels
3. Open channels
4. Gated channels


1. Chemically gated chemicals
2. Voltage-gated channels
3. Mechanically gated channels

What are the types of carrier-mediated transport & how many molecules do they transport?

Uniport - 1 kind of substrate

Symport - 2 or more substrates in **same** direction across membrane

Antiport - move substrates in opposite directions

Facilitated diffusion

Uses carrier proteins

* No energy input
* Down concentration gradient
* Conformational change

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Active transport

Uses carrier proteins

* Energy input, against concentration gradient
* Competition vs saturation